Mistrusted and Forgotten
by Rikki Writinglover
Summary: The Earth has been dominated before Atlantis could make it back the Pegasus, and Rodney has abandoned Atlantis to work for the bad guys. Or so they think. When John runs into Rodney after spending three years hating the man, he discovers they were all very, very wrong. Rodney saves John, and is welcomed back to Atlantis, but still it might not be enough to save him from himself.


It hadn't taken long for the world to crumble.

Shortly after Atlantis had arrived in the Milky Way and right before they went home to Pegasus, the Gould put the perfect plan in action.

They waited until Samantha Carter, Jack O'Neil, and Daniel Jackson were distracted helping for the preparations of Atlantis's return to Pegasus , and then kidnapped the three off guard, using them as the host bodies for three Gould, so they could use the human's skills to rule Earth. The three who use to be Jack, Daniel and Sam are back at SGC before anyone is the wiser. No one see's what they're planning until it's too late to stop them.

Under the brilliance of Jackson and Carter, and the firm military hand of O'Neil, Earth fell in minutes. Not without the help though, of one Rhodey McKay. Right before anyone knew what was going on, Rhodey disappeared off Atlantis, and the next thing his friends knew he was right hand man to the now evil and controlled SG1, Rodney himself free of alien influence. Everyone on Atlantis was dumbstruck; sure that Rodney was faking somehow, until Rodney designed a gas that killed Major Loren. In their grief, his old team, his colleges, forgot any faith they had in him and deemed him a traitor as they fought the tyranny in the Resistance.

Unfortunately, there weren't too many free willed people left to resist. Most of the military had been taken out of the equation when Sam and Rodney had developed a chip, which made them completely obedient. O'Neil had almost no problems getting it installed before the military were aware that he was no longer on their side.

Sam, Daniel, and Jack forced the population of Earth to kneel before them as Gods. No one ever saw Rodney with him, but Sam made sure to mention him as a "Loyal friend" almost every speech, and Radek knew Rodney's handiwork when he saw it.

John, Ronon, Teyla, Elizabeth, Carson, Ford, and Radek headed the Resistance, and as more of Rodney's creations put their friends in the infirmary or killed them outright; their hatred of the man they once loved like family grew. Except for Carson, whenever Elizabeth and John referred to him as a traitor, Carson made sure to remind them they didn't know for sure he wasn't possessed by the Gould. Or that he wasn't being controlled in some other way. Still, Elizabeth had a plan to assassinate the former SG1 team, Rodney included. Carson fought it, said they could capture him, and it came down to a vote. John, Elizabeth, Ronon and Ford voted to kill him. Carson, Teyla, and Radek voted no. Carson screamed his head off at John for willingly going to kill the man who used to be John's closet friend and John just told Carson that possessed or not, that Rodney was long gone, and he had people to protect.

That was why John had no qualms about his mission to be beamed inside the base Rodney, Sam, Jack, and Daniel lived in, and blow it all too hell. He got in and planted the bomb and everything was going fine until Rodney's security system kicked in and disabled it. Radek had warned him that as much as he hated to admit it he couldn't top Rodney and if he had set precautions, then there was no debate that Rodney could detect and disable it. Still John took the chance, he was prepared for failure, but not for the base to suddenly jam his tracking device and keep him from beaming out and escaping. Now, as the man who used to be Jack drags John towards Rodney's quarters, he has second thoughts.

Jack opens the door and throws John into the room, the rope burning on John's hands. Johns looks scans his surroundings to see Rodney gaping at him. John tries not to gasp at the man's appearance. Rhodey has lost so much weight that the sweater he's wearing is barely hanging on to his shoulders, his skin is pale and sickly looking. His eyes skim John nervously before turning towards Jack.

"Hello Jack. To what do I owe this pleasure?" Rodney stuttered quietly, and that was a shock that had John reeling and suspicious-Rhodey was never quiet. At least he never used to be. John reminded himself that this wasn't the man he thought he knew, this was a murderer, but the subdued tone of Rodney's voice hurt anyway.

Jack smirked at Rodney from the entrance and gestured towards John, who was lying on the carpet. "Just thought you'd want a little chat with you Ex- Teammate before we kill him, you have two hours Rhodey, as a little gift for all you do for us." John was surprised to see hatred flash in Rodney's eyes before he nodded and whispered "Thank you" To Jack. Jack just smiled and left, slamming the door behind him. John turned hateful eyes to Rodney, who immediately rushed over to him and dropped to his knees in front of him, eyes wide and concerned.

"John are you alright?!" Rodney spoke softly and comforting, as if the bastard hadn't betrayed him and gotten him into the situation in the first place. It was the same tone Rodney had used when they were friends and it was pissing John off immensely. He just glowered at the man and spit at his shoes.

"No McKay you bastard, I'm not! Why? Maybe because I'm face to face with the piece of shit that betrayed us and is responsible for the deaths of dozens of my friends, and thousands of innocents!" Rodney didn't even blink, his usually expressive face just tired as he nodded and ran his hand through his hair. He eyed John and mumbled quietly. "You're okay then. Alright that's good, you won't be limping then, make faster time that way…" John felt confusion and fury sweep through him; He didn't know what McKay was talking about, but he had been waiting to get his hands on the traitor for years now and he couldn't, and now Loren's murderer was only a few damn feet away.

Rodney crossed the room to his dresser and started pulling things out; supplies. Food, blankets, clothes, everything, and tossing them onto the big bed in the center of the room, hands shaking in a way that unnerved John. Rodney had always has steady hands no matter how stressed he was, but now there were tremors steadily rocking the other man's body. Again John had to push away his old loyalties and focus on hating Rodney. Before he did something stupid like feel guilty he had to kill him.

"What the hell are you doing?" John growled at him, shaking himself out of his thoughts. Rodney glanced over his shoulder at him and then turned his attention to the bed, grabbing a pack from underneath it and stuffing the supplies into it, speaking quietly and rushed. "Packing you supplies John." Rodney pulled a blaster and a gleaming knife out, sitting the gun on the bed and heading towards him with the knife.

John stiffened immediately, ready to struggle, when Rodney froze, looking him in the eyes as his brow furrowed. "Wait, you're going to kill me when I let you go right?" John just smirked and spit a "Hell yes." In his face before he could truly think about the fact he wanted Rodney to let him go so he could kill him. He expected Rodney to do the obvious and move away but he just nodded as if it didn't faze him at all and sank in front of John, not even trying to look him in the eye. "I better tell you how to get out of here first then. The blaster is just like Ronon's; I made it two weeks ago. Here's my access card, it will get you through most of the doors, but you need to get as far away from this base as you can. Nearest town is a day's walk North, it gets cold at night so I packed you some blankets and enough supplies to get you there. You need to get as far as possible within the hour though, my guard comes to check on me in 30 minutes, so if you disable the device on my wrist first, then you have that long until they find my body and start looking for me, but this place is gonna be blown all to hell within the hour regardless, so you need to get away as quickly as possible." Rodney instructed without emotion, just cool detachment.

John's brain stumbled to keep up and process what Rodney was saying before Rodney cut through the ropes and dropped the knife at John's feet, turning back to fall into the recliner in the corner, closing his eyes.

John grabbed the knife and Rodney's pass on the ground and stared, dumbfounded for a moment before remembering Rodney was a genius and could be screwing with his head easily.

He jumped up and crossed the room to Rodney, holding the knife to the man's throat and snarling at him, barley noticing that there was indeed a strange bracelet device on Rodney's wrist he hadn't seen before. "What the hell are you talking about? Guard? Explosion? Why are you helping me? Do you think this is going to keep you from a deserved death?!" John hissed confusion and hatred seeping into his voice.

Rodney's eyes fluttered open to stare at him calmly and his ocean eyes were so broken and different for just a moment John had to force himself not to jerk back in shock. Rodney just studied him for a moment and shrugged. "I rigged an explosion to go off in an hour, enough to kill everyone on this base. Sam, Jack, Daniel and I will be dead and the world free. The guard? They put him on duty so I don't have time to do anything they can't heal. I'm helping you because I really don't want you or any other innocent people to die, in an hour most of the staff is off base and the only people who will be left are Daniel, Jack, Sam and I. A few guards, but there's nothing I can do about it, as much as I want to. Now you really should get going before you get caught." John stepped a few feet backwards in shock, away from Rodney and only then did he notice the dried blood on the knife. "I-"He stuttered "I don't get it. Can't heal…. The blood… you… traitor… what were you torturing someone for them or something? Someone they wanted to make sure you didn't kill? Trying to redeem yourself McKay? "His hazel eyes were dark and distrusting as he kept the knife slightly raised towards the other man who just sat and stared at him.

Rodney chuckled darkly and watched John for a moment. "I only tortured someone who deserves it, and yes I guess you could say they didn't want him dead. No I'm not trying to redeem myself. John you really need to get out of here." John looked at Rodney thoughtfully for a moment and as he tried to put together pieces that didn't fit he started to wonder if he was missing information.

They sat at an impasse for another moment and Rodney's eyes started to flutter closed again, only to sudden spring open as he remembered something. "Oh yeah here this will keep you warmer if you want it. Don't have a jacket, sorry." Rodney said as he pulled his pull over over his head leaving him in his tank top undershirt and tossing the shirt to John's feet, lying back again and closing his eyes.

John's eyes grew wide and he didn't even look at the shirt as he studied Rodney's arms. There were cuts EVERYWHERE! Jagged, deep, numerous scars. John's first thought was torture, then he noticed the angle….. They were all self-inflicted. _"I only tortured someone who deserves it._" John's eyes suddenly went wide and he gasped, which caused Rodney's eyes to shoot open again worried. "John?! What's wrong are you okay?!"

John took a deep breath to control his growing anger and confusion and gave Rodney an icy glare. "Rodney McKay, I'm not sure what's going on, but I want the whole story from the time you left Atlantis until about 10 minutes ago and I swear to god if you lie to me…." He trailed off leaving the threat empty. Rodney opened his mouth to obviously tell John to get out again and then sighed, seeing the determined expression in John's features that meant he wasn't going anywhere.

"They had Jeanine. That night I got a video of her tied up and a voice telling me to sneak out of the city and go to Cheyanne Mountain or they would kill Jeanine. They said if I told anyone they would kill her before help arrived and I couldn't take the risk so I snuck out…. They did have her when I got there. All three of them were there, waiting for me. They kidnapped me the moment I walked in the door and the next thing I knew I was waking up here, with Sam smiling at me. She told me that as much as she hated to admit it, I was too big of a threat and was the only one who had a chance of beating her and Daniel's tech. They didn't want to kill me though, they wanted me to work for them and if I didn't, they would kill Jeanine. So I worked. I did everything they asked. They loved it too. They loved making me kill the lab techs that made mistakes, create weapons to use against people who were once my friends. I tried to create as many "Bugs" as possible to give people a chance to escape-"

John interrupted suddenly his eyes widening in revelation. "You! You were the "Glitch" That let Elizabeth escape last month!" Rodney just smiled weakly and sighed. "I'm glad to hear she's okay." John gestured for Rodney to continue as his heart sank hearing the truth him and everyone else should have expected instead of assuming Rodney a traitor. Carson had been right.

"After I heard one of the gasses that I created killed Loren, something snapped. This-" Rodney gestured to his arms tiredly. " – Started. They let me visit Jeanine occasionally, and as much as I tried to hide it from her, she finally found out. She begged me to just to stop, to stop killing people to protect her and I refused- I- I guess she decided- that it wasn't worth- wasn't worth it- because-"

Rodney suddenly broke off into a sob and John had his hand on Rodney's shoulder before he knew what was happening.

"Because right after she told me I didn't need to do this to myself for her- two days later she committed suicide."

"Holy Shit…." John whispered a sob catching in his own throat "Rodney I-"

Rodney held up his hand and continued.

"After that I quit caring and slit my wrists. Sam and Daniel found me though, and used a new piece of tech to save me. Since they couldn't use my sister against me anymore, they rounded up a bunch of children, and told me the deal was the same. I worked or the kids died. They also assigned me guards so I couldn't kill myself, and put this device on my wrist to alert them if my vitals got dangerous. I just killed more and more innocent people and cut more and more. They don't care as long as it won't kill me or affect my work. So that's how it's been since Jeanine killed herself two years ago. I stopped eating and sleeping the more people I slaughtered and enslaved, and Sam had a doctor put me on an I.V. until I ate, but then again they only made me eat enough to keep me alive, not healthy. It took me forever to make the blaster, I would have gone for a gun but they would know those materials were missing, completely ready to fry my damn brains so badly they wouldn't heal, when last week your Resistance freed the kids, and I could finally make a plan to kill them without putting innocents in danger. Of course, they don't even know I know about the children's rescue, which is why they aren't expecting us all to blow to bits in now about 40 minutes. Time for you to get away now John."

With that Rodney just laid back and closed his eyes again and John gaped. "What? Rodney just come with me!" Rodney's eyes opened and he shook his head slowly. "I'm not leaving Sheppard." John growled. "What do you MEAN you aren't leaving?!" Rodney just shook his head again. "What part of fry my damn brains didn't you get? Or that I killed innocent people, and am about to kill more? I don't deserve to make it through this and I don't want to live through it anyway."

John froze at the pure self-loathing in Rodney's voice. What the hell happened to the self -centered asshole with a heart of gold he used to know?!

"Rodney get your ass up- that wasn't your fault and I'm not letting you kill yourself!

Rodney just smiled softly. "I'm glad you don't want me to die Sheppard, however misguided that is, but I have wanted this for years and there's nothing you can do but save yourself and let me get what I have coming. Which is this and on the off chance that the explosion doesn't work? Whatever torture Jack can think up before he kills me."

John watches for a moment and sighs. "I'm sorry Rodney," He pretended to turn around so Rodney's eyes flutter closed again before swinging around and punching the other man hard in the face, and watching him slouch over out cold, and move to drape Rodney's alarmingly thin frame over his. "But you are not dying."

John's breathing was ragged as he finally got himself and Rodney out of that damn complex.

The pass had worked perfectly and he could see in the distance alarms going off in the now smaller looking complex, as they discovered Rodney was missing. He sat Rodney, who was obviously in bad shape before since he was still out cold, gently on the ground and sat down next to him. He watched the base carefully; he had been keeping time carefully. He hated that he wasn't trusting Rodney completely, but he had to watch the base go sky high. He had to be sure before he radioed to be beamed up. It was 10 minutes until Rodney said the bomb would blow.

John looked at the scientist laid out next to him and only now noticed the bruises splattered around the man's neck, as if someone had strangled him, and his fists clenched. John wasn't sure if Rodney had done it to himself or Jack had, but either way he was angry.

He had never let himself think too much about Rodney since he disappeared. He had known that he needed to push his feelings aside if the opportunity to kill McKay came up, so he put it in the back of his mind and ignored it. But now, seeing Rodney after so long, so broken, only now was he realizing how deeply he had missed him. He had missed the chess games, the stupid rants, the ego, and the crazy selflessness when it came down to it despite all his self- centered tendencies, the stuttering, the ridiculous fears, just Rodney being Rodney. He had been silently grieving for his best friend for three years now and he didn't even know it. Now as he saw the dark circles under Rodney's eyes, the bruises, the cuts, he felt the urge to throw up. He had given up on Rodney. When he was sent to the future Rodney had wasted most of his life trying to get John back and it hadn't taken but a matter of months for John to lose faith in Rodney. They could have tried to contact him, so he could tell them about Jeanine and the kids sooner, but they marked him as a traitor and moved on.

Now Rodney was suicidal. He wanted to believe it was just hopelessness, but the scars on Rodney's arms told him Rodney had gotten to a very, very bad place in his captivity.

Everything was silent for a few more minutes until finally, the compound he was just inside was bathed in a huge blast of light and an Earth- shattering roar, and then nothing was left but flames and ashes.

John took another look at Rodney and tears filled his eyes. Rodney had saved them all again. Just like he always did. He quickly pulled the radio he had snagged from the bag and clicked it on.

"Elizabeth?"

There was a slight pause before-

"_John!? What happened to you?!"_

_"_Yes. Elizabeth I was captured…. And rescued….I'll explain everything… just beam me and McKay up. He's a friend."

"_WHAT!?"_

"Elizabeth just trust me! He blew up that damn base and saved my life now get me and him up there!"

There was a moment of quiet before he was bathed in blue light and came face to face with a very angry Elizabeth Weir.

**So yall, this is a new fandom I recently started writing for, and no, I haven't forgotten my Avengers fics, I just wanted to write this.**


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